A liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection.

Chronic hepatitis B virus (HBV) infection affects 300 million patients worldwide1,2, in whom virus-specific CD8 T cells by still ill-defined mechanisms lose their function and cannot eliminate HBV-infected hepatocytes3-7. Here we demonstrate that a liver immune rheostat renders virus-specific CD8 T cells refractory to activation and leads to their loss of effector functions. In preclinical models of persistent infection with hepatotropic viruses such as HBV, dysfunctional virus-specific CXCR6+ CD8 T cells accumulated in the liver and, as a characteristic hallmark, showed enhanced transcriptional activity of cAMP-responsive element modulator (CREM) distinct from T cell exhaustion. In patients with chronic hepatitis B, circulating and intrahepatic HBV-specific CXCR6+ CD8 T cells with enhanced CREM expression and transcriptional activity were detected at a frequency of 12-22% of HBV-specific CD8 T cells. Knocking out the inhibitory CREM/ICER isoform in T cells, however, failed to rescue T cell immunity. This indicates that CREM activity was a consequence, rather than the cause, of loss in T cell function, further supported by the observation of enhanced phosphorylation of protein kinase A (PKA) which is upstream of CREM. Indeed, we found that enhanced cAMP-PKA-signalling from increased T cell adenylyl cyclase activity augmented CREM activity and curbed T cell activation and effector function in persistent hepatic infection. Mechanistically, CD8 T cells recognizing their antigen on hepatocytes established close and extensive contact with liver sinusoidal endothelial cells, thereby enhancing adenylyl cyclase-cAMP-PKA signalling in T cells. In these hepatic CD8 T cells, which recognize their antigen on hepatocytes, phosphorylation of key signalling kinases of the T cell receptor signalling pathway was impaired, which rendered them refractory to activation. Thus, close contact with liver sinusoidal endothelial cells curbs the activation and effector function of HBV-specific CD8 T cells that target hepatocytes expressing viral antigens by means of the adenylyl cyclase-cAMP-PKA axis in an immune rheostat-like fashion.

Yield of diagnostic testing in evaluating etiology and end organ effects of pediatric hypertension.

BACKGROUND: Current recommendations regarding the utility of diagnostic investigations for pediatric hypertension are based on limited evidence, leading to wide practice variation. The objective of this study was to characterize the cohort of children that may benefit from secondary hypertension workup, and determine the diagnostic yield of investigations. METHODS: This was a single-center, retrospective cohort study of 169 children aged 1-18 years referred between 2000 and 2015, to a tertiary pediatric nephrology center in Canada, for evaluation of hypertension. The number of investigations completed, abnormal findings, and diagnostic findings that helped establish hypertension etiology was determined. RESULTS: 56 children were diagnosed with primary and 72 children with secondary hypertension in the outpatient setting. Secondary hypertension was predominant at all ages except for obese adolescents ≥ 12 years. Half of children with traditional risk factors for primary hypertension, including obesity, were diagnosed with secondary hypertension. Kidney ultrasound had the highest yield of diagnostic results (19.8%), with no difference in yield between age groups (P = 0.19). Lipid profile had a high yield of abnormal results (25.4%) as part of cardiovascular risk assessment but was only abnormal in overweight/obese children. Echocardiogram had a high yield for identification of target-organ effects in hypertensive children (33.3%). CONCLUSION: A simplified secondary hypertension workup should be considered for all hypertensive children and adolescents. High yield investigations include a kidney ultrasound, lipid profile for overweight/obese children, and echocardiograms for assessment of target-organ damage. Further testing could be considered based on results of initial investigations for the most cost-effective management. A higher resolution version of the Graphical abstract is available as Supplementary information.

Acute Shoshin beriberi syndrome immediately post-kidney transplant with rapid recovery after thiamine administration.

Pediatric kidney transplant surgery is usually well tolerated, despite suboptimal physical conditioning that may result from uremia and nutritional deficiencies that accompany end-stage kidney failure. Nutritional supplementation is used to overcome such deficiencies, especially for children needing dialysis. Thiamine, a water-soluble vitamin also known as vitamin B1, is a critical cofactor in energy metabolism and may be competitively inhibited by the antimetabolite oxythiamine, a uremic toxin that accumulates in kidney failure. We report a case of a thiamine deficiency syndrome leading to overwhelming cardiac dysfunction, metabolic instability, and hemodynamic compromise, after otherwise uneventful kidney transplant surgery. Prior to transplant, this 14-year-old boy was treated with peritoneal dialysis and received thiamine supplementation. Post-transplant, the patient first developed hyperglycemia, then lactic acidosis, and subsequently hemodynamic instability despite escalating treatment with volume resuscitation and inotropic medication. He made a rapid and complete recovery after administration of IV thiamine. This is the first reported case of Shoshin beriberi syndrome in a pediatric kidney transplant recipient. Inadequate dialysis may have been a key factor, with toxin accumulation and thiamine transporter downregulation contributing to his status. Functional thiamine deficiency should be considered as a potential treatable cause of early post-transplant hemodynamic instability.

Improved electronic uniformity and nanoscale homogeneity in template-grown CsPbBr3 nanorods.

One-dimensional metal halide perovskites are among the most promising candidate materials for optoelectronic devices. However, the heterogeneity and fast degradation of perovskite nanowires (NWs) and nanorods (NRs) synthesized using conventional approaches impose a bottleneck for their optoelectronic applications. Recently, all-inorganic perovskite CsPbBr3 NRs with tailored dimensions, crafted using an amphiphilic bottlebrush-like block copolymer (BBCP) as nanoreactors, have demonstrated enhanced stabilities. Herein, we report the electronic investigation into these template-grown CsPbBr3 NRs using dielectric force microscopy (DFM), a contactless, nondestructive imaging technique. All freshly prepared CsPbBr3 NRs exhibited ambipolar behaviors for up to two months after sample synthesis. A transition from ambipolar to p-type behaviors occurred after two months, and nearly all NRs completed the transition within two weeks. Moreover, template-grown CsPbBr3 NRs displayed better nanoscale electronic homogeneity compared to their conventional counterparts. The improved electronic uniformity and nanoscale homogeneity place the template-grown CsPbBr3 NRs in a unique advantageous position for optoelectronic applications.

Fastphylo: fast tools for phylogenetics.

BACKGROUND: Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computational efficiency has been a constraint on the applicability of distance methods on very large problem instances. RESULTS: We present fastphylo, a software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix. We compare fastphylo with other neighbor joining based methods and report the results in terms of speed and memory efficiency. CONCLUSIONS: Fastphylo is a fast, memory efficient, and easy to use software suite. Due to its modular architecture, fastphylo is a flexible tool for many phylogenetic studies.

Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion.

MOTIVATION: The evolution of viruses is very rapid and in addition to local point mutations (insertion, deletion, substitution) it also includes frequent recombinations, genome rearrangements and horizontal transfer of genetic materials (HGTS). Evolutionary analysis of viral sequences is therefore a complicated matter for two main reasons: First, due to HGTs and recombinations, the right model of evolution is a network and not a tree. Second, due to genome rearrangements, an alignment of the input sequences is not guaranteed. These facts encourage developing methods for inferring phylogenetic networks that do not require aligned sequences as input. RESULTS: In this work, we present the first computational approach which deals with both genome rearrangements and horizontal gene transfers and does not require a multiple alignment as input. We formalize a new set of computational problems which involve analyzing such complex models of evolution. We investigate their computational complexity, and devise algorithms for solving them. Moreover, we demonstrate the viability of our methods on several synthetic datasets as well as four biological datasets. AVAILABILITY: The code is available from the authors upon request.

Multiple sclerosis risk perception and acceptance for Brazilian patients.

The perception of multiple sclerosis (MS) severity and risk associated with therapies might influence shared decision making in different countries. We investigated the perception of MS severity and factors associated with risk acceptance in Brazil in 96 patients with relapsing-remitting MS using a standardized questionnaire and compared this with two European cohorts. Multiple sclerosis was perceived as a very severe disease and the risk of developing progressive multifocal leukoencephalopathy due to natalizumab was seen as moderate to high. Seventy-six percent considered a risk of 1:1,000, or higher, an impediment for natalizumab use. Older age was the only variable associated with higher risk acceptance and our patients showed a more conservative profile than German and Spanish patients. Our patients perceived MS severity and progressive multifocal leukoencephalopathy risk similarly to elsewhere, but their willingness to take risks was more conservative. This should be considered when discussing therapeutic options and it might have an impact on guideline adaptations.

Fast computation of distance estimators.

BACKGROUND: Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise distances between all pairs of taxa. Distance methods themselves are often fast, e.g., the famous and popular Neighbor Joining (NJ) algorithm reconstructs a phylogeny of n taxa in time O(n3). Unfortunately, the fastest practical algorithms known for Computing the distance matrix, from n sequences of length l, takes time proportional to l.n2. Since the sequence length typically is much larger than the number of taxa, the distance estimation is the bottleneck in phylogeny reconstruction. This bottleneck is especially apparent in reconstruction of large phylogenies or in applications where many trees have to be reconstructed, e.g., bootstrapping and genome wide applications. RESULTS: We give an advanced algorithm for Computing the number of mutational events between DNA sequences which is significantly faster than both Phylip and Paup. Moreover, we give a new method for estimating pairwise distances between sequences which contain ambiguity Symbols. This new method is shown to be more accurate as well as faster than earlier methods. CONCLUSION: Our novel algorithm for Computing distance estimators provides a valuable tool in phylogeny reconstruction. Since the running time of our distance estimation algorithm is comparable to that of most distance methods, the previous bottleneck is removed. All distance methods, such as NJ, require a distance matrix as input and, hence, our novel algorithm significantly improves the overall running time of all distance methods. In particular, we show for real world biological applications how the running time of phylogeny reconstruction using NJ is improved from a matter of hours to a matter of seconds.

Reconstruction of ancestral genomic sequences using likelihood.

A challenging task in computational biology is the reconstruction of genomic sequences of extinct ancestors, given the phylogenetic tree and the sequences at the leafs. This task is best solved by calculating the most likely estimate of the ancestral sequences, along with the most likely edge lengths. We deal with this problem and also the variant in which the phylogenetic tree in addition to the ancestral sequences need to be estimated. The latter problem is known to be NP-hard, while the computational complexity of the former is unknown. Currently, all algorithms for solving these problems are heuristics without performance guarantees. The biological importance of these problems calls for developing better algorithms with guarantees of finding either optimal or approximate solutions. We develop approximation, fix parameter tractable (FPT), and fast heuristic algorithms for two variants of the problem; when the phylogenetic tree is known and when it is unknown. The approximation algorithm guarantees a solution with a log-likelihood ratio of 2 relative to the optimal solution. The FPT has a running time which is polynomial in the length of the sequences and exponential in the number of taxa. This makes it useful for calculating the optimal solution for small trees. Moreover, we combine the approximation algorithm and the FPT into an algorithm with arbitrary good approximation guarantee (PTAS). We tested our algorithms on both synthetic and biological data. In particular, we used the FPT for computing the most likely ancestral mitochondrial genomes of hominidae (the great apes), thereby answering an interesting biological question. Moreover, we show how the approximation algorithms find good solutions for reconstructing the ancestral genomes for a set of lentiviruses (relatives of HIV). Supplementary material of this work is available at www.nada.kth.se/~isaac/publications/aml/aml.html.

Settling the intractability of multiple alignment.

Multiple alignment is a core problem in computational biology that has received much attention over the years, both in the line of heuristics and hardness results. In most expositions of the problem it is referred to as NP-hard and references are given to one of the available hardness results. However, previous to this paper not even the most elementary variation of the problem, multiple alignment under the unit metric, had been proved hard. The aim of this paper is to settle the NP-hardness of the most common variations of multiple alignment. The following variations are shown NP-hard for all metrics over binary or larger alphabets: MULTIPLE ALIGNMENT WITH SP-SCORE, STAR ALIGNMENT, and TREE ALIGNMENT (for a given phylogeny). In addition, NP-hardness results are provided for CONSENSUS PATTERNS and SUBSTRING PARSIMONY.

A 1.375-approximation algorithm for sorting by transpositions.

Sorting permutations by transpositions is an important problem in genome rearrangements. A transposition is a rearrangement operation in which a segment is cut out of the permutation and pasted in a different location. The complexity of this problem is still open and it has been a 10-year-old open problem to improve the best known 1.5-approximation algorithm. In this paper, we provide a 1.375-approximation algorithm for sorting by transpositions. The algorithm is based on a new upper bound on the diameter of 3-permutations. In addition, we present some new results regarding the transposition diameter: we improve the lower bound for the transposition diameter of the symmetric group and determine the exact transposition diameter of simple permutations.

Agents of non-gonococcal urethritis in males attending an Israeli clinic for sexually transmitted diseases.

BACKGROUND: Non-gonococcal urethritis is the most common clinical diagnosis in men seeking care at clinics for sexually transmitted diseases. OBJECTIVE: To identify the pathogens involved in NGU among males attending an Israeli STD clinic. METHODS: During 19 months spanning September 1996 to July 1998 we investigated a cohort of 238 male patients attending the Bnai Zion Medical Center STD clinic with a clinical presentation of urethritis. Intraurethral swab specimens were tested for Neisseria gonorrhea, Ureaplasma urealyticum, Mycoplasma hominis, and Trichomonas vaginalis by culture and for herpes simplex virus by antigen detection. First voiding urine for C. trachomatis was done by polymerase chain reaction. The specific seropositivities of HSV types 1 and 2 were tested by enzyme-linked immunosorbent assay. RESULTS: From among 238 males with dysuria or urethral discharge an etiology for urethritis was found for 71 (29.8%). N. gonorrhea was recovered in only three men (4.2%). In the remaining 68 NGU patients Chlamydia trachomatis (35/68, 51.5%) and U. urealyticum (31/68, 45.6%) were the most common infecting and co-infecting pathogens (P < 0.0001). M. hominis and T. vaginalis were found in 9/68 (13.2%), and 1 patient, respectively. HSV was recovered from the urethra in 7/68 males (10.3%)--3 with HSV-1, 2 with HSV-2, and 2 were seronegative for HSV. None of these males had genital lesions. Although a single etiologic agent was identified in 45/68 infected men (66.2%), co-infection was common: 2 organisms in 15 (22%) and 3 organisms in 8 (11.8%). CONCLUSION: C. trachomatis and U. urealyticum were the most common infecting and co-infecting pathogens in this cohort of men with NGU. Unrecognized genital HSV infections are common in males attending our STD clinic, and symptomatic shedding of HSV occurs without genital lesions. Still, the microbial etiology in this group remains unclear in many patients despite careful microbiologic evaluation.

Multiple sclerosis risk perception and acceptance for Brazilian patients / Percepção e aceitação de risco em pacientes brasileiros com esclerose múltipla

ABSTRACT The perception of multiple sclerosis (MS) severity and risk associated with therapies might influence shared decision making in different countries. We investigated the perception of MS severity and factors associated with risk acceptance in Brazil in 96 patients with relapsing-remitting MS using a standardized questionnaire and compared this with two European cohorts. Multiple sclerosis was perceived as a very severe disease and the risk of developing progressive multifocal leukoencephalopathy due to natalizumab was seen as moderate to high. Seventy-six percent considered a risk of 1:1,000, or higher, an impediment for natalizumab use. Older age was the only variable associated with higher risk acceptance and our patients showed a more conservative profile than German and Spanish patients. Our patients perceived MS severity and progressive multifocal leukoencephalopathy risk similarly to elsewhere, but their willingness to take risks was more conservative. This should be considered when discussing therapeutic options and it might have an impact on guideline adaptations.

RESUMO A percepção de gravidade da esclerose múltipla (EM) e riscos associado a terapias podem influenciar a escolha de tratamento em diferentes países. Investigamos a percepção da gravidade da EM e fatores associados à aceitação de risco em 96 pacientes com EM remitente-recorrentecom um questionário e comparamos com duas coortes europeias. A EM foi percebida como muito grave e o risco de desenvolver leucoencefalopatia multifocal progressiva devido ao natalizumabe, como moderado a alto, sendo que76% consideraram um risco de 1: 1.000 ou maior como impeditivo deseu uso. Idade mais avançada foi a única variável associada àaceitação de risco mais elevado e nossos pacientes revelaram um perfil mais conservador do que os pacientes alemães e espanhóis. Esses dados devem ser considerados ao discutir opções terapêuticas e pode ter impacto nas adaptações de diretrizes locais.

Stomatin-like protein 2 binds cardiolipin and regulates mitochondrial biogenesis and function.

Stomatin-like protein 2 (SLP-2) is a widely expressed mitochondrial inner membrane protein of unknown function. Here we show that human SLP-2 interacts with prohibitin-1 and -2 and binds to the mitochondrial membrane phospholipid cardiolipin. Upregulation of SLP-2 expression increases cardiolipin content and the formation of metabolically active mitochondrial membranes and induces mitochondrial biogenesis. In human T lymphocytes, these events correlate with increased complex I and II activities, increased intracellular ATP stores, and increased resistance to apoptosis through the intrinsic pathway, ultimately enhancing cellular responses. We propose that the function of SLP-2 is to recruit prohibitins to cardiolipin to form cardiolipin-enriched microdomains in which electron transport complexes are optimally assembled. Likely through the prohibitin functional interactome, SLP-2 then regulates mitochondrial biogenesis and function.

Innate immunity mediated by TLR5 as a novel antiinflammatory target for cystic fibrosis lung disease.

Novel therapies to target lung inflammation are predicted to improve the lives of people with cystic fibrosis (CF) but specific antiinflammatory targets have not been identified. The goal of this study was to establish whether TLR5 signaling is the key molecular pathway mediating lung inflammation in CF, and to determine whether strategies to inhibit TLR5 can reduce the damaging inflammatory response. The innate immune responses were analyzed in both airway epithelial cells and primary PBMCs from CF patients and matched controls. Additionally, 151 clinical isolates of Pseudomonas aeruginosa from CF patients were assessed for motility and capacity to activate TLR5. Blood and airway cells from CF patients produced significantly more proinflammatory cytokine than did control cells following exposure to the CF pathogens P. aeruginosa and Burkholderia cepacia complex (p < 0.001). Stimulation with pure TLR ligands demonstrated that TLR signaling appears to mediate the excessive cytokine production occurring in CF. Using complementary approaches involving both neutralizing Ab targeting TLR5 and flagellin-deficient bacteria, we established that inhibition of TLR5 abolished the damaging inflammatory response generated by CF airway cells following exposure to P. aeruginosa (p < 0.01). The potential therapeutic value of TLR5 inhibition was further supported by our demonstration that 75% of clinical isolates of P. aeruginosa retained TLR5 activating capacity during chronic CF lung infection. These studies identify the innate immune receptor TLR5 as a novel antiinflammatory target for reducing damaging lung inflammation in CF.